The Department for Education has released figures showing 2.5% of pupils were off school on September 30 due to Covid-19.
Over 200,000 pupils were absent from state-schools in the two weeks prior to September 30, the BBC reports.
Schools returned this September without many covid restrictions as the government wanted to maximise the time pupils could spend in the classroom.
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Absence rates in the autumn before the pandemic were around 4.5% but that has risen to 13.7% in secondary schools since pupils returned.
A spokesperson for the Department of Education said: "We are working with parents and school and college staff to maximise students' time in the classroom - encouraging uptake of testing and the vaccine for 12-15-year-olds, and contracting specialist attendance advisers to work on strategies to improve attendance where problems are identified.
"If there are particularly high Covid case rates in a school or college, local directors of public health may advise they reintroduce additional temporary measures such as increased testing or face coverings - but face-to-face education should be prioritised."
Under current guidlines in schools only pupils who test positive for the virus have to go home and isolate - neither close contacts of confirmed Covid cases or bubble groups have to go home and isolate.
The DfE statistics showed:
- 102,000 pupils (1.3%) had a confirmed case of Coronavirus, up 72%, from 59,000 the last time the figures were released, on 16 September
- 84,000 pupils (1.0% of pupils) were absent with a suspected case of Covid
- 5,000 were absent because of restrictions to manage a Covid outbreak
- 2,000 were absent because of Covid-related school closures
- 11,000 were isolating for other reasons
Liz Lord, a headteacher of a school in West Yorkshire said: "It feels like a normal school again, but at the same time, we're dealing with, unfortunately, a rise in the number of Covid cases.
"It causes concern and it causes worry. The number of school Covid cases is higher than it was in the summer.
"But it hasn't got the same level of disruption, because we're not sending kids around the person who is ill home to self-isolate any more."
Geoff Barton, Association of School and College Leaders general secretary is writing to the Education Secretary in a bid to see what can be done about the rise in cases.
He said: "These grim statistics show a big increase in the number of pupils out of school as a result of the continuing havoc caused by Coronavirus.
"We are hearing from schools where there are 10% or more of pupils absent and where staff are also off work because of the virus.
"Teaching and learning is very difficult in these circumstances and it is clear that the educational disruption of the past 18 months is far from being over."
General secretary Paul Whiteman said: "School leaders want the government to revisit its guidance, particularly when it comes to contact tracing and self-isolation.
"No-one wants to see a child miss any time off school but there is a real risk that the current policy is inadvertently leading to more children missing school in the long run."
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